NBDC Research ID: hum0340.v1
SUMMARY
Aims: Compared to adult cancer, pediatric cancer has an extremely small number of patients and a wide range of diseases, so the genetic and epigenetic abnormalities have not been fully elucidated. Our hospital is one of the 15 pediatric cancer base hospitals nationwide. We have experienced a large number of relapsed / refractory cancer cases, and detailed clinical information on each case is also preserved. We conducted a comprehensive genomic analysis using tumor tissue, non-tumor tissue, and germline tissue of pediatric solid tumor patients which we experienced at our hospital. In addition, we will clarify the abnormalities peculiar to pediatric cancer by comparing them with the genomic information of adult cancer cases.
Methods: We developed more efficient DNA extraction methods using FFPE tissues of pediatric and adult cancer patients and compared the data from whole genome sequencing (WGS) analysis and target capture sequencing (TCS) analysis.
Participants/Materials:
[WGS]
・Colorectal cancer：24 cases (FFPE non-tumor tissues)
・Retinoblastoma：1 case (FFPE tumor tissues)
[TCS]
・Glioblastoma：2 cases (peripheral blood, fresh frozen tumor tissues, and FFPE tumor tissues)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000520 | NGS（WGS, Target Capture） | Controlled-access (Type I) | 2022/08/04 |
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MOLECULAR DATA
| Participants/Materials |
Adult colorectal cancer (ICD10: C189)：24 cases FFPE non-tumor tissues: 28 samples Child retinoblastoma (ICD10: C692)：1 case FFPE tumor tissues: 3 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Hiseq X Ten] |
| Library Source | DNAs extracted from FFPE normal tissues and FFPE tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Thru PLEX DNA-Seq Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100-200 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000640 |
| Total Data Volume | 175.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Adult glioblastoma (ICD10 : C719)：2 cases blood cells: 2 samples fresh frozen tumor tissues: 2 samples FFPE tumor tissues: 8 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | 127 mutated genes implicated across 12 tumor tissue types (xGen® Pan-Cancer Panel v1.5) |
| Platform | Illumina [Hiseq X Ten] |
| Library Source | DNAs extracted from peripheral blood cells, fresh frozen tumor tissues, and FFPE tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Thru PLEX DNA-Seq Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000640 |
| Total Data Volume | 175.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Utako Oba
Affiliation: Department of Pediatrics, Kyusyu University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections | doi: 10.1093/biomethods/bpac014 | JGAD000640 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
